Variant report

Variant	rs10440116
Chromosome Location	chr3:52275042-52275043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52273987-52275172	HL-60	blood:	n/a	n/a
2	POLR2A	chr3:52273968-52275278	Raji	blood:	n/a	n/a
3	EP300	chr3:52274022-52275085	K562	blood:	n/a	n/a
4	KAP1	chr3:52274021-52275163	HEK293	kidney:	n/a	n/a
5	POLR2A	chr3:52274036-52275183	PANC-1	pancreas:	n/a	n/a
6	USF1	chr3:52274634-52275056	K562	blood:	n/a	n/a
7	POLR2A	chr3:52274088-52275163	GM12891	blood:	n/a	n/a
8	POLR2A	chr3:52273816-52275204	U87	brain:	n/a	n/a
9	POLR2A	chr3:52272974-52275139	PBDE	blood:	n/a	n/a
10	MTA3	chr3:52272162-52275133	GM12878	blood:	n/a	n/a
11	CEBPB	chr3:52274193-52275165	IMR90	lung:	n/a	n/a
12	MAX	chr3:52273856-52275294	HCT-116	colon:	n/a	n/a
13	BHLHE40	chr3:52274611-52275124	K562	blood:	n/a	n/a
14	POLR2A	chr3:52272416-52275284	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr3:52271840-52275220	HepG2	liver:	n/a	n/a
16	TCF12	chr3:52273947-52275199	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr3:52273887-52275204	U87	brain:	n/a	n/a
18	POLR2A	chr3:52273897-52275066	U87	brain:	n/a	n/a
19	MAFF	chr3:52274835-52275194	K562	blood:	n/a	n/a
20	POLR2A	chr3:52274076-52275215	HCT-116	colon:	n/a	n/a
21	POLR2A	chr3:52273959-52275197	U87	brain:	n/a	n/a
22	MAFK	chr3:52274921-52275199	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:52274465-52275240	HepG2	liver:	n/a	n/a
24	KAP1	chr3:52274152-52275266	U2OS	brain:	n/a	n/a
25	POLR2A	chr3:52273851-52275422	HCT-116	colon:	n/a	n/a
26	POLR2A	chr3:52273942-52275298	SK-N-MC	brain:	n/a	n/a
27	GATA3	chr3:52274460-52275144	SH-SY5Y	brain:	n/a	n/a
28	NFIC	chr3:52274735-52275406	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr3:52274878-52275363	HCT-116	colon:	n/a	n/a
30	NFATC1	chr3:52274359-52275052	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:52273977-52276440	K562	blood:	n/a	n/a
32	CEBPB	chr3:52274210-52275096	K562	blood:	n/a	n/a
33	ZMIZ1	chr3:52274504-52275044	K562	blood:	n/a	n/a
34	GATA2	chr3:52274614-52275409	SH-SY5Y	brain:	n/a	n/a
35	POLR2A	chr3:52273945-52275208	SK-N-SH	brain:	n/a	n/a
36	GATA1	chr3:52274176-52275399	PBDE	blood:	n/a	n/a
37	USF1	chr3:52274565-52275080	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr3:52272765-52275094	H1-hESC	embryonic stem cell:	n/a	n/a
39	TEAD4	chr3:52274507-52275201	K562	blood:	n/a	n/a
40	RCOR1	chr3:52274023-52275267	K562	blood:	n/a	n/a
41	NFIC	chr3:52274625-52275320	ECC-1	luminal epithelium:	n/a	n/a
42	ARID3A	chr3:52274626-52275065	K562	blood:	n/a	n/a
43	MAX	chr3:52274507-52275051	K562	blood:	n/a	n/a
44	USF1	chr3:52274687-52275056	SK-N-SH_RA	brain:	n/a	n/a
45	RUNX3	chr3:52274403-52275203	GM12878	blood:	n/a	n/a
46	TAL1	chr3:52274638-52275089	K562	blood:	n/a	n/a
47	JUND	chr3:52274055-52275100	K562	blood:	n/a	n/a
48	SETDB1	chr3:52274601-52275150	U2OS	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52272619..52275147-chr3:52443057..52446254,5	K562	blood:
2	chr3:52006492..52009228-chr3:52273747..52276252,2	K562	blood:
3	chr3:52271022..52275105-chr3:52320320..52325575,6	K562	blood:
4	chr3:52270811..52276588-chr3:52310648..52314131,11	K562	blood:
5	chr3:52027463..52030131-chr3:52273399..52277503,3	K562	blood:
6	chr3:52269470..52276026-chr3:52310334..52314212,10	MCF-7	breast:
7	chr3:52274866..52276465-chr3:52300888..52302569,2	MCF-7	breast:
8	chr3:52269533..52276077-chr3:52310385..52313504,11	MCF-7	breast:
9	chr3:52272181..52276088-chr3:52318615..52323958,11	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPM1M-2	chr3:52274191-52275813	NONHSAT089901

No data

Variant related genes	Relation type
TWF2	TF binding region
TLR9	TF binding region
PPM1M	TF binding region
ENSG00000168237	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000199150	Chromatin interaction
ENSG00000272762	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000248487	Chromatin interaction
ENSG00000114786	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10212380	1.00[EUR][1000 genomes]
rs10212560	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17052143	1.00[EUR][1000 genomes]
rs28413740	1.00[EUR][1000 genomes]
rs28434358	1.00[EUR][1000 genomes]
rs28636773	1.00[EUR][1000 genomes]
rs34540591	1.00[EUR][1000 genomes]
rs5743834	1.00[EUR][1000 genomes]
rs9813448	1.00[EUR][1000 genomes]
rs9813468	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9813489	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813653	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9815559	1.00[EUR][1000 genomes]
rs9821916	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9824342	1.00[EUR][1000 genomes]
rs9828432	1.00[EUR][1000 genomes]
rs9828488	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9831689	1.00[EUR][1000 genomes]
rs9834363	1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9836166	1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9842960	0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9843055	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9844178	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9845752	1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9857947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9863874	1.00[EUR][1000 genomes]
rs9868332	1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv876791	chr3:52269491-52286825	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52273800-52275200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52273800-52275200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
3	chr3:52273800-52275200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:52273800-52275400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr3:52273800-52275400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr3:52274000-52275200	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr3:52274000-52275200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:52274000-52275200	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr3:52274000-52275200	Flanking Active TSS	GM12878-XiMat	blood
10	chr3:52274000-52275400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:52274000-52275400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:52274000-52275400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:52274200-52275200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:52274200-52275200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:52274200-52275200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr3:52274200-52275200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:52274200-52275200	Enhancers	Brain Hippocampus Middle	brain
18	chr3:52274200-52275200	Enhancers	NHDF-Ad	bronchial
19	chr3:52274200-52275400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr3:52274200-52275400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr3:52274200-52275600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:52274400-52275200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr3:52274400-52275200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:52274400-52275200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:52274400-52275200	Enhancers	Adipose Nuclei	Adipose
26	chr3:52274400-52275200	Enhancers	Brain Angular Gyrus	brain
27	chr3:52274400-52275200	Enhancers	Brain Substantia Nigra	brain
28	chr3:52274400-52275200	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr3:52274400-52275200	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr3:52274400-52275200	Enhancers	Hela-S3	cervix
31	chr3:52274400-52275200	Enhancers	HMEC	breast
32	chr3:52274400-52275200	Enhancers	HSMM	muscle
33	chr3:52274400-52275200	Transcr. at gene 5' and 3'	K562	blood
34	chr3:52274400-52275200	Enhancers	Osteobl	bone
35	chr3:52274400-52275400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr3:52274400-52275800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr3:52274400-52276000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr3:52274400-52276600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr3:52274400-52276600	Enhancers	Fetal Thymus	thymus
40	chr3:52274400-52278800	Weak transcription	Fetal Lung	lung
41	chr3:52274400-52279000	Weak transcription	Fetal Heart	heart
42	chr3:52274400-52279400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52274600-52275200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr3:52274600-52275200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:52274600-52275200	Genic enhancers	A549	lung
46	chr3:52274600-52275400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:52274600-52275400	Enhancers	Thymus	Thymus
48	chr3:52274600-52276400	Enhancers	Primary T cells from cord blood	blood
49	chr3:52274600-52276400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:52274600-52277600	Weak transcription	Primary hematopoietic stem cells	blood

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